Since you mention OTA, I'm assuming you're trying to download the application onto your BlackBerry by entering a URL into a browser that points to your JAD file (i.e., you've launched a browser on your BlackBerry, and you entered a URL into it that looks something like: http://www.mywebserver/blackberry/myapp/MyApp.jad
So my first question is: which browser application on the BlackBerry are you using?
The reason I asked which browser you're using is that sometimes using the carrier-specific browser (Media.Net for AT&T devices, etc.) with COD/JAR modules that are > 64K will cause failure in the download process. Only the RIM browser seems to consistently download large-size (> 64K) applications.
Another issue that may be problematic for you: if the contents of your JAD file are only what's listed above, you are missing the SHA1 signatures of the COD files, and that's probably what's causing the "907 Invalid COD HTTP Error 406: Not Acceptable" response. There should be a line that looks like: RIM-COD-SHA1: 12 34 56 78 9a bc de f0 19 2a 3b 4c 5d 6e 7f 80 aa bb cc dd
where the 20 hexadecimal pairs are the SHA-1 hash of the module. There should be one line like this for each COD file in the JAD.
If you split up the JAR file into its component .class files in their hierarchy, you can use the RAPC compiler to stitch them back together. I would also rename the original JAD file so that the RAPC compiler is forced to produce a completely new one, and then you can add the other things to the new JAD file from the old one that RAPC missed out on (things like the icon, etc.).
Note: All of the parts of the "assumption" I've mentioned above should really be answered ahead of time in your post - the more information you provide up front (model number, OS version, carrier, APN settings, etc., as well as the precise steps you followed and the results/response at each step) the quicker your question can get answered. With BlackBerry development - especially what amounts to effectively cross-platform (J2ME vs. BlackBerry Java) - there are a lot of different ways things can go wrong, and those of us out here in the aether can make better guesses as to what's happening the more information you give us.